Relevant bibliographies by topics / Ligand Molecules

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Ligand Molecules'

Author: Grafiati
Published: 7 September 2023
Last updated: 31 July 2025

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Journal articles on the topic "Ligand Molecules"

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Zhou, Mengbo, Li Song, Feng Niu, Kangying Shu та Wenxiang Chai. "A square-pyramidal copper(II) complex with strong intramolecular hydrogen bonds: diaqua(N,N′-dimethylformamide-κO)bis[2-(diphenylphosphoryl)benzoato-κO]copper(II)". Acta Crystallographica Section C Crystal Structure Communications 69, № 5 (2013): 463–66. http://dx.doi.org/10.1107/s0108270113008317.

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In the title CuIIcomplex, [Cu(C19H14O3P)2(C3H7NO)(H2O)2], the molecule is bisected by a twofold axis relating the two 2-(diphenylphosphoryl)benzoate (ODPPB) ligands. The asymmetric unit consists of a CuIImetal centre on the symmetry axis, an ODPPB ligand, one water ligand and one dimethylformamide (DMF) ligand (disordered around the twofold axis). The CuIIion has fivefold coordination provided by two carboxylate O atoms from two ODPPB ligands, two O atoms from two coordinated water molecules and another O atom from a (disordered) DMF molecule, giving a CuO5square-pyramidal coordination geometr
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Suwardi, Suwardi, Agus Salim, Joanda Ario Yudha Mahendra, et al. "Virtual Screening, Pharmacokinetic Prediction, Molecular Docking and Dynamics Approaches in the Search for Selective and Potent Natural Molecular Inhibitors of MAO-B for the Treatment of Neurodegenerative Diseases." Indonesian Journal of Chemistry and Environment 6, no. 2 (2023): 95–110. http://dx.doi.org/10.21831/ijoce.v6i2.68338.

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This research aims to find natural product compounds that have the potential to act as MAO-B inhibitors that are useful in the treatment of neurodegenerative diseases, through the stages: a) Virtual Screening, b) Molecule Docking, c) Pharmacokinetic and toxicity prediction, and d) Simulation approach Molecular dynamics.The research steps include the following steps: a) searching for molecules in the ZINC15 data base that are similar to the natural ligand molecule (safinamide) obtained from the protein data bank (PDB code: 2v5z) and the control ligand L-DOPA. A total of 481 molecules were downl
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Nagamalla, Lavanya, J. V. Shanmukha Kumar, Mohammed Rafi Shaik, et al. "Identification of Novel AXL Kinase Inhibitors Using Ligand-Based Pharmacophore Screening and Molecular Dynamics Simulations." Crystals 12, no. 8 (2022): 1158. http://dx.doi.org/10.3390/cryst12081158.

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AXL kinase is a promising target in novel drug discovery for cancer. A ligand-based pharmacophore model was generated with the Pharmit web server. Its inbuilt PubChem molecule database was screened and led to 408 candidate molecules. Docking of the AXL kinase active sites with the identified list of candidate molecules was carried out with Autodock Vina docking software. This resulted in four compounds selected for further investigation. Molecular dynamics simulation of two ligands (PubChem-122421875 and PubChem-78160848) showed considerable binding with AXL kinase. From the MM-PBSA binding fr
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Kim, Yun Young, та Joseph M. Tanski. "Crystal structure of a rare trigonal bipyramidal titanium(IV) coordination complex: trichlorido(3,3′-di-tert-butyl-2′-hydroxy-5,5′,6,6′-tetramethyl-1,1′-biphenyl-2-olato-κO2)(tetrahydrofuran-κO)titanium(IV)". Acta Crystallographica Section E Crystallographic Communications 73, № 1 (2017): 88–91. http://dx.doi.org/10.1107/s2056989016020156.

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The title compound, [Ti(C24H33O2)Cl3(C4H8O)], is a rare example of a trigonal–bipyramidal titanium coordination complex with three chloride and two oxygen donor ligands. The asymmetric unit contains two independent molecules having essentially the same conformation. The molecules feature the titanium(IV) metal cation complexed with three chloride ligands, a tetrahydrofuran molecule, and one oxygen atom from the resolved ligand precursor (R)-(+)-5,5′,6,6′-tetramethyl-3,3′-di-t-butyl-1,1′-biphenyl-2,2′-diol, where the remaining phenolic hydrogen atom engages in intermolecular O—H...Cl hydrogen b
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Lie, W. R., N. B. Myers, J. M. Connolly, J. Gorka, D. R. Lee, and T. H. Hansen. "The specific binding of peptide ligand to Ld class I major histocompatibility complex molecules determines their antigenic structure." Journal of Experimental Medicine 173, no. 2 (1991): 449–59. http://dx.doi.org/10.1084/jem.173.2.449.

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To better understand the biological implications of the association of ligand with major histocompatibility complex class I molecules, we have studied the Ld molecule of the mouse. The culturing of various nonselected cell lines with three different known Ld peptide ligands resulted in a two- to fourfold specific increase in surface Ld expression as detected by 10 of 11 different monoclonal antibodies (mAbs) recognizing Ld epitopes. These findings suggest that Ld molecules are not saturated with endogenous peptide ligands and thus have accessible binding sites. Exploiting this feature of Ld we
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Baisya, Siddhartha S., та Parag S. Roy. "(2-Amino-7-methyl-4-oxidopteridine-6-carboxylato-κ3O4,N5,O6)aqua(ethane-1,2-diamine-κ2N,N′)nickel(II) dihydrate". Acta Crystallographica Section E Structure Reports Online 69, № 2 (2013): m99—m100. http://dx.doi.org/10.1107/s160053681300069x.

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The NiIIatom in the title complex, [Ni(C8H5N5O3)(C2H8N2)(H2O)]·2H2O, is six-coordinated in a distorted octahedral geometry by a tridentate 2-amino-7-methyl-4-oxidopteridine-6-carboxylate (pterin) ligand, a bidentate ancillary ethane-1,2-diamine (en) ligand and a water molecule. The pterin ligand forms two chelate rings. The en and pterin ligands are arranged nearly orthogonally [dihedral angle between the mean plane of the en molecule and the pterin ring = 77.1 (1)°]. N—H...O, O—H...N and O—H...O hydrogen bonds link the complex molecules and lattice water molecules into a three-dimensional net
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Yardan, Alper, and Cenk Paşa. "Spectroscopic, Crystallographic and Thermal Comparison of Two Asymmetric Tridentate Schiff Base Molecules." International Journal of Nature and Life Sciences 8, no. 2 (2024): 228–40. https://doi.org/10.47947/ijnls.1591265.

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Two similar asymmetric ONO type tridentate Schiff Base ligand molecules and their spectroscopic, crystallographic and thermal properties are comparised. Both of molecules obtained in the study were characterized by 1H-NMR, 13C-NMR, thermal analysis, IR spectroscopy and UV-Vis spectroscopy. However molecules were able to be obtained as single crystals and their structures were determined by single crystal X-ray technique. The space group of the geometric shape of the 2'-(2-hydroxy-anilidene)-4-hydroxy-pentane (L1) ligand is P212121. There are 4 molecules in the unit cell of the crystal system o
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Gupta, Shivani. "Investigation of anti-microbial activity of imidazol [2, 1-B][1,3,4] thiadiazole by using molecular docking and ADMET studies." Indian Journal of Pharmacy and Pharmacology 9, no. 3 (2022): 201–4. http://dx.doi.org/10.18231/j.ijpp.2022.036.

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This report consists of molecular docking based on series of imidazol [2,1-b], , thiadiazole-benzimidazole derivative. Molecular docking is software which gives information about molecular modeling in which molecule fits into target binding sites and predict structure of intermolecular complex. These molecules were investigated by protein ligand binding score, protein ligand interaction and ADME studies. All the target molecules were analyzed against which is a gram positive bacteria found on skin and upper respiratory tract. The protein molecule selected for the analysis was PDB code 4LAE pro
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Koehler, Melanie, Anny Fis, Hermann J. Gruber, and Peter Hinterdorfer. "AFM-Based Force Spectroscopy Guided by Recognition Imaging: A New Mode for Mapping and Studying Interaction Sites at Low Lateral Density." Methods and Protocols 2, no. 1 (2019): 6. http://dx.doi.org/10.3390/mps2010006.

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Ligand binding to receptors is one of the most important regulatory elements in biology as it is the initiating step in signaling pathways and cascades. Thus, precisely localizing binding sites and measuring interaction forces between cognate receptor–ligand pairs leads to new insights into the molecular recognition involved in these processes. Here we present a detailed protocol about applying a technique, which combines atomic force microscopy (AFM)-based recognition imaging and force spectroscopy for studying the interaction between (membrane) receptors and ligands on the single molecule le
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Salio, Mariolina, Wael Awad, Natacha Veerapen, et al. "Ligand-dependent downregulation of MR1 cell surface expression." Proceedings of the National Academy of Sciences 117, no. 19 (2020): 10465–75. http://dx.doi.org/10.1073/pnas.2003136117.

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The antigen-presenting molecule MR1 presents riboflavin-based metabolites to Mucosal-Associated Invariant T (MAIT) cells. While MR1 egress to the cell surface is ligand-dependent, the ability of small-molecule ligands to impact on MR1 cellular trafficking remains unknown. Arising from an in silico screen of the MR1 ligand-binding pocket, we identify one ligand, 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoic acid, DB28, as well as an analog, methyl 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoate, NV18.1, that down-regulate MR1 from the cell surface and re
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Dissertations / Theses on the topic "Ligand Molecules"

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Orro, Graña Adolfo. "Examination of the role of binding site water molecules in molecular recognition." Thesis, SciLifeLab Stockholm, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-200164.

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A set of algorithms were designed, implemented and evaluated in order to, first, identifyclusters of conserved waters in binding pockets, i.e. hydration sites. Then, their contributionto the free energy of binding in a ligand-protein association was quantified by calculatingtheir enthalpy and entropy. The information obtained by using these algorithms couldcontribute to the development of new drugs by generating new ligands that target specifichigh-energy, unfavorable waters. Evaluation tests show that our algorithms can indeedprovide relevant data about how hydration sites influence ligand-pr
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Homeyer, Alexander von. "A superimposition method for small ligand molecules implementation and application /." [S.l.] : [s.n.], 2007. http://deposit.ddb.de/cgi-bin/dokserv?idn=984854991.

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Charmant, Jonathan Paul Henry. "Reactivity of the #mu#3-benzyne ligand towards small organic molecules." Thesis, University of Bristol, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.238905.

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Ambrosek, David Hunter. "Quantum optimal control of bond selective separation of ligands from organometallic molecules." Berlin dissertation.de, 2007. http://www.dissertation.de/buch.php3?buch=5262.

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Eremina, Nadejda. "Infrared spectroscopic studies : from small molecules to large." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-101077.

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Infrared light (IR) was first discovered by Friedrich Wilhelm Herschel in 1800. However, until 1940’s, molecular IR studies involved only water and small organic molecules, because of the long measurement times. Development Fourier transform infrared spectroscopy (FTIR) has minimized the time required to obtain data, making it possible to investigate bigger biological systems, e.g. proteins and nucleic acids.This thesis concentrates on the applications of different IR spectroscopic techniques to a variety of biological systems and development of new approaches to study complicated biological e
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Morris, Daniel L. "NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY IN THE STUDY OF PROTEIN-LIGAND INTERACTIONS." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron1524681449524557.

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Sarangapani, Krishna Kumar. "Characterizing selectin-ligand bonds using atomic force microscopy (AFM)." Diss., Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/11650.

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The human body is an intricate network of many highly regulated biochemical processes and cell adhesion is one of them. Cell adhesion is mediated by specific interactions between molecules on apposing cell surfaces and is critical to many physiological and pathological processes like inflammation and cancer metastasis. During inflammation, blood-borne circulating leukocytes regularly stick to and roll on the vessel walls, which consist in part, adhesive contacts mediated by the selectin family of adhesion receptors (P-, E- and L-selectin). This is the beginning of a multi-step cascade that ult
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Renberg, Björn. "Fluorescence-based ligand assays for protein detection using affibody affinity proteins." Doctoral thesis, KTH, Skolan för bioteknologi (BIO), 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3936.

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The detection and quantification of biomolecules, and proteins in particular, are of great interest since these molecules are of fundamental importance to our well-being. Body fluids, as for instance human blood, are well suited for sampling of protein levels. However, the complexity of the fluids and the low abundance of many of the interesting biomolecules makes detection and quantification difficult. This has spurred an interest into the development of many protein detection methods, and of these, ligand assays have proven particularly suitable. In this thesis, different types of ligand ass
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Zhang, Fang. "Two-dimensional binding kinetics of intracellular adhesion molecule-1 for αL inserted domains and β₂ integrins at different conformational states". Thesis, Georgia Institute of Technology, 2004. http://hdl.handle.net/1853/9452.

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Zhang, Fang. "Two-dimensional binding kinetics of intracellular adhesion molecule-1 for [alpha]L inserted domains and [beta]₂ integrins at different conformational states." Available online, Georgia Institute of Technology, 2004:, 2004. http://etd.gatech.edu/theses/available/etd-06072004-131425/unrestricted/zhang%5Ffang%5F200405%5Fms.pdf.

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Books on the topic "Ligand Molecules"

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Höltje, Hans-Dieter. Molecular modeling: Basic principles and applications. VCH, 1997.

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Joel, Sussman, and Spadon Paola, eds. From molecules to medicines: Structure of biological macromolecules and its relevance in combating new diseases and bioterrorism. Springer, 2009.

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J, Beuth, and Pulverer Gerhard, eds. Lectin blocking: New strategies for the prevention and therapy of tumor metastasis and infectious diseases : proceedings of the Intern. Symposium Otzenhausen, May 8-9, 1993. Fischer, 1994.

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Hans-Dieter, Höltje, ed. Molecular modeling: Basic principles and applications. 3rd ed. VCH, 2008.

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Symposium on Host-Guest Molecular Interactions: from Chemistry to Biology (1990 : Ciba Foundation), ed. Host-guest molecular interactions: From chemistry to biology. Wiley, 1991.

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J, Langone John, ed. Molecular design and modeling: Concepts and applications. Academic Press, 1991.

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Roterman, Irena, and Leszek Konieczny, eds. Self-Assembled Molecules – New Kind of Protein Ligands. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-65639-7.

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1944-, Langone John J., ed. Molecular design and modeling: Concepts and applications. Part A, Proteins, peptides, and enzymes. Academic Press, 1991.

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Hans-Joachim, Böhm, and Schneider Gisbert 1965-, eds. Protein-ligand interactions from molecular recognition to drug design. Wiley-VCH, 2003.

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Siegfried, Schwarz. Molecules of life & mutations: Understanding diseases by understanding proteins. Karger, 2002.

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Book chapters on the topic "Ligand Molecules"

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Cremer, Julian, Tuan Le, Djork-Arné Clevert, and Kristof T. Schütt. "Latent-Conditioned Equivariant Diffusion for Structure-Based De Novo Ligand Generation." In Lecture Notes in Computer Science. Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-72381-0_4.

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AbstractWe propose PoLiGenX for de novo ligand design using latent-conditioned, target-aware equivariant diffusion. Our model leverages the conditioning of the generation process on reference molecules within a protein pocket to produce shape-similar de novo ligands that can be used for target-aware hit expansion and hit optimization. The results of our study showcase the efficacy of PoLiGenX in ligand design. Docking scores indicate that the generated ligands exhibit superior binding affinity compared to the reference molecule while preserving the shape. At the same time, our model maintains
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Baron, Riccardo, Piotr Setny, and J. Andrew McCammon. "Hydrophobic Association and Volume-Confined Water Molecules." In Protein-Ligand Interactions. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527645947.ch8.

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Eble, Johannes A. "Integrins—A Versatile and Old Family of Cell Adhesion Molecules." In Integrin-Ligand Interaction. Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-4064-6_1.

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Freund, Hans-Joachim. "Clean and Modified Oxide Surfaces: Structure and Dynamics of Absorbed Molecules." In Metal-Ligand Interactions. Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0155-1_9.

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Prakash, Om, and Feroz Khan. "CoSSDb: A Database of Co-crystallized Ligand Sub-structures for Anticancer Lead Designing & Optimization." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022). Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_14.

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AbstractThe Discovery of the novel optimized structures of small molecules for selective targeting is one of the challenging tasks in drug designing. Bioisosteres are the key components of the lead compound, which provide hidden power to the compound scaffold for selective targeting. We are presenting a database, named CoSSDb which stands for Co-crystallized Sub-Structure Database. The CoSSDb contains ligand sub-structures as possible bioisosteres. extracted from PDB files, available in Protein Data Bank. Sub-structures were extracted through an algorithm, which utilizes the location of atoms
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Sherwood, Amanda R., Vikas V. Dukhande, Matthew S. Gentry, et al. "Ligand-Dependent Nuclear Receptor Corepressor (LCoR)." In Encyclopedia of Signaling Molecules. Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4419-0461-4_100705.

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van Roy, Frans, Volker Nimmrich, Anton Bespalov, et al. "Chemokine (C-X-C Motif) Ligand 10." In Encyclopedia of Signaling Molecules. Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4419-0461-4_100260.

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Karplus, Martin. "Dynamics of Ligand Binding to Proteins." In Design and Synthesis of Organic Molecules Based on Molecular Recognition. Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-70926-5_8.

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Teraoka, J., N. Yamamoto, Y. Matsumoto, Y. Kyogoku, and H. Sugeta. "Vibrational Circular Dichroism of Ligand Vibrations in Hemeprotein." In Spectroscopy of Biological Molecules. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0371-8_106.

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Freund, H. J., T. Klüner, R. Wichtendahl, et al. "Molecules on Clean and Modified Oxide Surfaces." In Metal-Ligand Interactions in Chemistry, Physics and Biology. Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4245-8_5.

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Conference papers on the topic "Ligand Molecules"

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Azizah, Ninna Arifatun Nurul, Sentot Budi Rahardjo, Witri Wahyu Lestari, and Soerya Dewi Marliyana. "Synthesis and Characterization of Copper Complex Chelated with Phenobarbital Ligand." In 8th International Conference on Advanced Material for Better Future. Trans Tech Publications Ltd, 2025. https://doi.org/10.4028/p-n2rlar.

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The research is intended to synthesize copper(II) with Phenobarbital (PB) complex in 1 : 4 mole ratio. The sole reflux method is designated to synthesize reactant within methanol solvent. Cu(II) complex is characterized using Atomic Absorption Spectrophotometry (AAS), UV-Vis Spectrophotometer, Fourier-transform Infrared Spectroscopy (FTIR), Thermogravimetric Analysis (TGA), Conductivity meter, and Magnetic Susceptibility Balance (MSB). The Cu(II)-PB complex signified 1 absorption peak at 517.5 nm with 2Eg → 2T2g transition. Complex is then composed by 6 electron donors of Cu ion-bound ligand,
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Lv, Xing, Weizhong Zhao, Xinhui Tu, and Tingting He. "Predicting Protein-ligand Binding Affinity via Molecular Mechanics-guided Graph Aggregation." In 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2024. https://doi.org/10.1109/bibm62325.2024.10822564.

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Gao, Yandong, Dana Brantley-Sieders, Devi Majumdar, Jin Chen, Donna Webb, and Deyu Li. "A Simple Approach to Probe the Extracellular Signaling Pathways Using Ligand Traps." In ASME 2012 Third International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/mnhmt2012-75106.

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Cells communicate with one another through a huge variety of extracellular soluble signaling molecules. A common method in biology to investigate the signaling pathways is to inactivate the gene coding the interested ligand or receptor from cells using modern DNA technology, known as gene knockout. Even though very effective, however, gene knockout is a time-consuming and cost-prohibitive process and requires huge amount of efforts to conduct. Here we present a simple method to probe the extracellular signaling pathways through engineering a semi-permeable barrier between two cell populations.
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Brewer, Bryson M., Yandong Gao, Rebecca M. Sappington, and Deyu Li. "Microfluidic Molecular Trap: Probing Extracellular Signaling by Selectively Blocking Exchange of Specific Molecules in Cell-Cell Interactions." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-64489.

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Communication among cell populations is achieved via a wide variety of soluble, extracellular signaling molecules [1]. In order to investigate the role of specific molecules in a cellular process, researchers often utilize in vitro cell culture techniques in which the molecule under question has been removed from the signaling pathway. Traditionally, this has been accomplished by eliminating the gene in the cell that is responsible for coding the targeted ligand/receptor by using modern DNA technology such as gene knockout; however, this process is expensive, time-consuming, and labor intensiv
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Steimle, Timothy C., Boa-Zhong Li, and Kook Young Jung. "Molecular Beam Optical Stark and PPMODR Spectroscopy of Pt Containing Molecules." In Modern Spectroscopy of Solids, Liquids, and Gases. Optica Publishing Group, 1995. http://dx.doi.org/10.1364/msslg.1995.ssaa4.

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Ligated platinum compounds are important in many homogeneous catalytic processes yet there is very little experimental information about the Pt-ligand bond. The most detailed information about bonding comes from the analysis of gas phase spectra recorded at a resolution sufficient to resolve the fine and hyperfine structure and shifts in spectral features caused by the application of static electric and magnetic fields. The advent of the supersonic laser ablation/reaction source (1-4) has eliminated many of the problems associated with the generation molecules containing refractory elements, s
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Morozkina, Svetlana N., Petr P. Snetkov, and Mayya V. Uspenskaya. "Docking of Small Molecules with in Vivo Cardiovascular Activity into The Proteins – The Relationship with Side-Effects." In International Medicine and Health Sciences Congress. ECER, 2024. https://doi.org/10.53375/imhsc.2024.35.

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Cardiac amyloidosis is a clinical pathology, usually of a genetically mediated nature, initiated by the formation of amyloid fibrils, that lead to death. The number of clinically used molecules for the treatment of cardiac amyloidosis is very limited with strong side effects (for example, tafamidis and diflunisal). In this study, the methods of molecular modeling and computer docking of ligands using ICM-pro (Molsoft LLS, USA) were used to evaluate for the first time the level of side binding of small molecules possessing in vivo cardiovascular activity into the ligand-binding domains of 136 p
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Boboriko, Natalia, He Liying, and Yaraslau Dzichenka. "THE EXPLORATION OF CYP17A1 LIGAND SPACE BY THE QSAR MODEL." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.439b.

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Cytochrome P450 17A1 (CYP17A1) is a critically important enzyme in humans that catalyzes the formation of all endogenous androgens. This enzyme is often considered a molecular target for the development of novel high efficient drugs against prostate cancer. In the present work, the random forest algorithm was used to conduct a QSAR study on 370 CYP17A1 ligands with different structures that were collected from the literature and databases, and a QSAR model was created based on the five important descriptors screened out – 2D adjacency and distance matrix descriptors, 2D atom counts and bond co
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Stevanović, Kristina, Draginja Radošević, Vladimir Perović та Sanja Glišić. "Combined in silico approach to identify new terpenoid PPARα agonists". У 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.601s.

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In treating atherosclerosis and dyslipidemia, peroxisome proliferator-activated receptor alpha (PPARα) has been recognized as an interesting drug target. It is a ligand-activated transcriptional factor that controls genes involved in lipid metabolism regulation. The discovery of natural PPARα agonists may open new perspectives in its targeting. For several terpenoid molecules, it has been shown that they potentially activate PPARα. Linalool is a terpenoide molecule for which the PPARα antagonistic effect has been demonstrated in vivo. Here, we focused on searching for new terpenoid PPARα agoni
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Chesla, Scott E., Bryan T. Marshall, and Cheng Zhu. "Measuring the Probability of Receptor Extraction From the Cell Membrane." In ASME 1997 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1997. http://dx.doi.org/10.1115/imece1997-0262.

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Abstract Recently, there has been an increasing interest in measuring the interaction forces between cell adhesion receptors and their ligands [1–3]. These molecules are either anchored on the membrane of a cell or coated on the surface of a substratum. The two surfaces are joined together as a result of the formation of non-covalent bonds between the receptors and ligands. The forces are measured when the two surfaces are separated. In a theoretical paper published nineteen years ago, George Bell estimated the force required to break a receptor-ligand bond and that required to uproot the rece
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Alsawaf, Shahed, Tuğba Bal, and Zihni Onur Çalışkaner. "EXPLORING THE POTENTIAL OF DRUG REPURPOSING AGAINST ABNORMALLY REGULATED CELL-MATRIX INTERACTIONS IN THE TREATMENT OF PANCREATIC CANCER (A COMPUTATIONAL STUDY)." In STRA International Conference on Engineering & Technology, 09-10 October 2024, Istanbul. Global Research & Development Services, 2024. https://doi.org/10.20319/icstr.2024.9192.

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Pancreatic ductal adenocarcinoma (PDAC) represents one of the most aggressive cancers, with a 5-year survival rate of only 8%. The progression of the disease is significantly influenced by the tumor microenvironment, especially by cell-extracellular matrix (ECM) interactions. The aim of this study is to repurpose small molecules as inhibitor candidates to jointly target key receptors for the ECM attachment, specifically discoidin domain receptors (DDR1 and DDR2), which are implicated in promoting tumor growth through cell-collagen interactions.Using a computational drug repurposing framework,
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Reports on the topic "Ligand Molecules"

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บุญรัตนกรกิจ, วิโรจน์. ตัวจับของโปรเจสเตอโรนหยุดยั้งการเติบโตของเซลล์มะเร็งปอดโดยการรบกวนการส่งสัญญาณของ Epidermal growth factor receptor (EGFR). จุฬาลงกรณ์มหาวิทยาลัย, 2016. https://doi.org/10.58837/chula.res.2016.42.

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ในปัจจุบันเริ่มมีหลักฐานว่า progesterone receptor (PR) มีความเกี่ยวข้องกับมะเร็งปอดชนิด NSCLC อย่างไรก็ตามยังไม่มีการศึกษาเกี่ยวกับกลไกการส่งสัญญาณของ PR กับ NSCLC โดยจากการศึกษาที่ผ่านมาพบว่า PR มี Polyproline SH3 recognition motif (PXXPXR motif หรือ PPD) ที่สามารถจับกับ SH3 domain ของ signaling molecules ได้ ผู้วิจัยจึงตั้งสมมุติฐานว่า PXXPXR motif ของ PR สามารถขัดขวางการส่งสัญญาณของ EGFR ผ่าน MAPK และ/หรือ AKT pathway ในเซลล์มะเร็งปอดได้ ซึ่งจะส่งผลให้เซลล์มะเร็งปอดมีการเจริญเติบโตลดน้อยลง โดยทำการทดสอบบทบาทของ PXXPXR motif ในด้านการเจริญเติบโตและการส่งสัญญาณในเซลล์มะเร็งปอดที่มีการแสดงออกข
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Scavuzzo, Sebastian, Jonathan Cedeño, and Jaroslava Miksovska. In Silico Calculation of Interhelical Angles in NCS1. Florida International University, 2025. https://doi.org/10.25148/fiuurj.3.1.16.

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Proteins are important macromolecules responsible for a variety of processes in living organisms. One of the most important features of proteins is their ability to respond to environmental stimuli, such as changes in intracellular metal concentration by binding metal ions, which in turns triggers structural changes within the protein that can modify its function or allow the protein to participate in a signaling pathway. One such signaling protein is the so-called neuronal calcium sensor 1 protein or NCS1, which binds Ca2+ along with other abiogenic metals such as Li+, and the metal binding r
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Leeladee, Pannee. Cooperative small-molecule activation toward sustainable catalysis. Faculty of Science, Chulalongkorn University, 2018. https://doi.org/10.58837/chula.res.2018.47.

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In this research, a series of copper complexes containing polypyridyl ligands were designed to study the influence from ligands, nuclearity, solvents and secondary coordination on reactivity toward small-molecule activation. This structure-reactivity relationship was used in investigation for oxygen reduction reactions (ORR), and applied in detection of ascorbic acid (AsH₂). Firstly, copper (II) complexes containing polypyridyl derivatives ligands (i.e., Cu(dpa), Cu(adpa) and Cu₂ (addpa)) were synthesized and fully characterized by elemental analysis, mass spectrometry and X-ray crystallograph
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Yedidia, I., H. Senderowitz, and A. O. Charkowski. Small molecule cocktails designed to impair virulence targets in soft rot Erwinias. United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134165.bard.

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Chemical signaling between beneficial or pathogenic bacteria and plants is a central factor in determining the outcome of plant-microbe interactions. Pectobacterium and Dickeya (soft rot Erwinias) are the major cause of soft rot, stem rot, and blackleg formed on potato and ornamentals, currently with no effective control. Our major aim was to establish and study specific bacterial genes/proteins as targets for anti-virulence compounds, by combining drug design tools and bioinformatics with experimental work. The approach allowed us to identify and test compounds (small molecules) that specific
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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mut
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Cutler, A. R. Selective transformation of carbonyl ligands to organic molecules. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/5021885.

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Kumar, Aishani, Thendral Yalini, and Sunil Kumar C. Unlocking Cellular Control: The Promise of PROTACs in Disease Intervention. Science Reviews - Biology, 2024. http://dx.doi.org/10.57098/scirevs.biology.3.2.1.

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The discovery of proteolysis-targeting chimeras (PROTACs) is among the most exciting and promising avenues in cancer therapy. These fascinating compounds signify a paradigm shift from traditional approaches to medication development, offering a new idea that leverages the complexities of biological mechanisms to accomplish highly focused degradation of particular proteins implicated in pathological processes. This novel strategy has the potential to address a number of drawbacks with conventional therapy techniques, such as the development of drug resistance and unexpected adverse effects resu
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Diaz Arenas, Carolina. Evolutionary Dynamics in Molecular Populations of Ligase Ribozymes. Portland State University Library, 2000. http://dx.doi.org/10.15760/etd.44.

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Montal, Mauricio. Channel Protein Engineering: A Novel Approach towards the Molecular Dissection Determinants in Ligand-Regulated Channels. Defense Technical Information Center, 1990. http://dx.doi.org/10.21236/ada219134.

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Kemp, Richard, Timothy J. Boyle, Jeffery A. Greathouse, et al. Detection of Soluble Ligand-Tuned Molecular Tags for Subterranean Fluid Flow Monitoring Using Resonance Raman Spectroscopy. Office of Scientific and Technical Information (OSTI), 2017. http://dx.doi.org/10.2172/1603849.

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